Main
Patrick Cherry
PhD scientist skilled in bioinformatics, biological data science, data visualization, statistical modeling, next-generation sequencing (NGS), and tool-building. I’ve coded reproducible and rigorous pipelines for high-throughput experimental designs and genomic analyses, launched best-in-class oncology reference standards, and invented new molecular methods for DNA and microbe manipulation. Originally trained in Molecular Biology, I’m interested in taking my knowledge and practice of data science / bioinformatics to the next level, especially on spatial and single cell data analysis.
Education
PhD
University of Colorado School of Medicine
Aurora/Denver, Colorado
2019 - 2013
- Ph.D. in Molecular Biology
- Advisor: Jay Hesselberth, PhD.
- Thesis: RNA Terminus chemistry affects the decay events that target HAC1 mRNA during the Unfolded Protein Response
BA
Hendrix College
Conway, Arkansas
2013 - 2009
- Biochemistry and Molecular Biology, with Distinction
- Advisor: Andres Caro, PhD.
- Senior Capstone Project showing key stress response gene expression changes to oxidative stress in liver cells
- Minor in Mathematics; PI: Lars Seme; Project: Newton’s method as a fractal chaotic dynamical system
Industry Experience
I currently split my time between wet lab and computational activities. I have worked in a variety of roles ranging from HTP strain onboarding to genomics scientist. I like collaborative environments where I can learn from my peers and in turn teach others.
Senior Scientist
Twist Bioscience
South San Francisco, California
Current - 2022
- Tech Lead of multiple reference control NPIs, custom OEMs, and commercial releases. Includes the Pan-cancer RNA Fusion Controls, Fragmentome Calibration Controls, CNV Controls, Pan-cancer cfDNA v2, and RNA-seq.
- Mentored a direct report from Senior Research Associate to Scientist to serving as a Tech Lead on new product introductions
- Original research led to multiple outside presentations and applications for patent protection of product configuration and biochemical methods.
- Custom data analysis pipeline in R and Python demonstrated proof-of-concept design and QC success of the Pan-cancer RNA Fusion Controls; designed and implemented the production approach; used public databases and feedback from alpha testers to design configuration of fusions RNAs
- Led new technology evaluation of a new NGS platform with custom experiments and bioinformatic analyses in Python, R, and SQL to enable faster gene QC in Production. Also led ancillary experiments to speed up synthetic gene production. Coded, implemented, and distributed on company GitHub an internal package,
twistcolorpal, that automatically adds Twist-brand colors toggplot2plots and sets up database connectors toSQL/ Snowflake for parameterizeddbplyrquerying. Regularly use R, tidyverse, Python, Polars, AWSs3,Spark,PySpark, andSparklyr, locally and on Databricks.
Scientist
Twist Bioscience
South San Francisco, California
Current - 2021
- Tech Lead of Pan-Cancer Reference Standard, an ISO-13485 synthetic positive control with 458 unique variants among 84 cancer-associated genes at six QC’d VAFs, plus a WT control, which launched in Nov of 2021
- Designed, implemented, & validated primer removal procedure for DNA standards that is compatible with methylation
- Devised and validated precise high-throughput DNA quantification process for accurate pooling
- Led multiple iterations of custom NGS analysis refined the QC approach and thresholds for ensuring a contamination-free production process; extensively used data visualization to communicate complex data to cross-functional collaboration teams.
- Made extensive use of UMI sequencing and created novel method to rigorously quantify library conversion efficiency to evaluate product and potential secondary sources
Scientist I
Zymergen, Inc.
Emeryville, California
2021 - 2019
- Designed and implemented an automated high-throughput genotyping assay
- Designed & carried out complex experiments on automation with and without LIMS sample tracking
- Supported a company-wide NGS core under high demand from diverse groups with complex needs using data-driven decision making and teaching
- Used statistical methods to screen and optimize a genetic engineering protocol for newly-on-boarded microbe; delivered robust process while working on New Product Introduction team
- Built hundreds of plasmids using modern molecular cloning techniques like Gibson and Golden Gate
Research Experience
I worked on a few projects during my PhD, and the RNA repair project led me to custom 5´-OH RNA-seq libraries, which inspired my fascination with transcriptomics and bioinformatics.
Doctoral Research
University of Colorado School of Medicine
Aurora/Denver, Colorado
2019 - 2014
- Wrote, revised, & published two academic papers on RNA repair & yeast genetics
- Engineered and characterized genetic bypass of essential genes in budding yeast; on-boarded CRISPR/Cas9 for efficient and precise gene knock-in
- Expressed, purified, and used wild-type and mutant recombinant protein in E. coli to carry out an RNA modification enzymatic assay
- Optimized custom RNA-seq library protocol; independently planned, executed, troubleshooted RNA modification detection
- Routinely conducted northern blotting, targeted depletion, primer extension, splinted ligation, and other esoteric DNA and RNA experiments
Intellectual Property
Working at Twist and Zymergen on new product research requires confidentiality, but public evidence of accomplishments often comes in patent applications. The Legal teams know me well for being a helpful expert in the process.
Methylation-mediated adapter removal on nucleic acid sequences
Twist Bioscience
South San Francisco, California
3/7/23
- US 63/317,466
Expansion of cfDNA for Libraries
Twist Bioscience
South San Francisco, California
11/12/21
- US Prov. Pat. Ref No 823.102
Libraries for mutational analysis
Twist Bioscience
South San Francisco, California
4/9/21
- US Prov. Pat. Ref No 823.101
Method for counterselection in microorganisms
Zymergen, Inc.
Emeryville, California
3/25/21
- US 2021_0087586 A1
Selected Publications
I communicate my results clearly, both in writing and in live presentations. I enjoy writing research papers, but my career has required more tech notes and app notes recently.
Twist Pan-cancer synthetic reference materials technical guide
South San Francisco, California
12/21/21
- Patrick Cherry & Mike Bocek
Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response
N/A
2019
- Cherry, P., Peach, S., & Hesselberth, J.
Genetic bypass of essential RNA repair enzymes in budding yeast
N/A
2018
- Cherry, P., White, L., York, K., & Hesselberth, J.
Selected Presentations & Talks
I give audience-centered presentations by adapting on the fly and over time to the venue and occasion. I like to transfer knowledge by giving methods/best practices talks whose slides can also serve as documentation.
High sensitivity detection of specific ultra low-frequency somatic mutations for minimal residual disease (MRD) monitoring
International Society of Liquid Biopsy Annual Congress
Madrid, Spain
11/19/23
Twist pan-cancer synthetic RNA fusion control for assay development
American Association for Cancer Researchers
Orlando, Florida
4/16/23
Use of synthetic CNV fragments to mimic copy number alterations for ctDNA reference standards
Advances in Genome Biology and Technology
Hollywood, Florida
2/7/23
Twist pan-cancer synthetic reference materials for cell-free DNA (cfDNA) assay development
American Association for Cancer Researchers
New Orleans, Louisiana
4/12/22
Molecular Methods Meet the Standards: Or how I learned to stop worrying and love UV-quantification
Twist R&D Meeting
South San Francisco, CA
7/13/21
R use at Zymergen
Z-Tech Talk
Emeryville, CA
6/16/20
Data-driven troubleshooting of NGS experiments
Data Science Talk
Emeryville, CA
4/20/20